Splicing and Junction Mapping

Alternative splicing plays a major role in regulating the functional repertoire of the proteome. However, isoform-specific effects to protein-protein interactions (PPIs) are usually overlooked, making it impossible to judge the functional role of individual exons on a systems biology level. ...

University of Oxford researchers present VALERIE (Visualising alternative splicing events from single-cell ribonucleic acid-sequencing experiments), an R package for visualising alternative splicing events at single-cell resolution. To explore any given specified genomic region, corresponding to an alternative splicing event, VALERIE ...

Genomic rearrangements can modify gene function by altering transcript sequences, and have been shown to be drivers in both cancer and rare...

To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, researchers at St. Jude Children’s Research Hospital have developed CICERO, a local assembly-based algorithm that integrates...

Researchers at CHOP and University of Pennsylvania developed an online tool to refine results from RNA sequencing obtained from clinically accessible tissuesDNA sequencing is becoming a more commonplace method for detecting diseases and improving...

RNA sequencing experiments generate large amounts of information about expression levels of genes. Although they are mainly used for quantifying expression levels, they contain much more biologically important information such as copy number variants (CNVs). Researchers from the University of ...

Circular RNAs (circRNAs), covalently closed continuous RNA loops, are generated from cognate linear RNAs through back splicing events, and alternative splicing events may generate different circRNA isoforms at the same locus. However...

Alternative splicing alterations have been widely related to several human diseases revealing the importance of their study for the success of translational medicine. Differential splicing (DS) occurrence has been mainly analyzed through...

Differential splicing (DS) is a post-transcriptional biological process with critical, wide-ranging effects on a plethora of cellular activities and disease processes. To date, a number of computational...

Gene fusions can generate immunogenic neoantigens that mediate anticancer immune responses. However, their computational prediction from RNA sequencing (RNA-seq) data requires deep bioinformatics expertise to assembly a computational workflow covering the prediction of: fusion transcripts, their translated proteins and peptides, Human Leukocyte Antigen (HLA) types, and peptide-HLA binding ...